[svn-r22105] Description:

	Bring r20557:22085 from trunk to this branch, also fixing some other
issues/failures in the branch simultaneously.  The h5repack tests are still
failing, but Neil will be checking into those, so the branch can be fully
functional again.

Tested on:
	Mac OSX/64 10.7.3 (amazon) w/debug

1 files changed, 55 insertions, 31 deletions

diff --git a/tools/h5repack/h5repack.c b/tools/h5repack/h5repack.c
index 1e7e0ed..05160d8 100644
--- a/tools/h5repack/h5repack.c
+++ b/tools/h5repack/h5repack.c
@@ -91,7 +91,7 @@ h5repack_init(pack_opt_t *options, int verbose, int latest,
     H5F_file_space_type_t strategy, hsize_t threshold)
 {
     int k, n;
-    memset(options,0,sizeof(pack_opt_t));
+    HDmemset(options,0,sizeof(pack_opt_t));
     options->min_comp = 1024;
     options->verbose  = verbose;
     options->latest = latest;
@@ -110,7 +110,7 @@ h5repack_init(pack_opt_t *options, int verbose, int latest,
     return (options_table_init(&(options->op_tbl)));
 }
 
-
+
 /*-------------------------------------------------------------------------
 * Function: h5repack_end
 *
@@ -124,7 +124,7 @@ int h5repack_end  (pack_opt_t *options)
     return options_table_free(options->op_tbl);
 }
 
-
+
 /*-------------------------------------------------------------------------
 * Function: h5repack_addfilter
 *
@@ -159,7 +159,7 @@ int h5repack_addfilter(const char* str,
         if(options->n_filter_g > H5_REPACK_MAX_NFILTERS)
         {
             error_msg("maximum number of filters exceeded for <%s>\n", str);
-            free(obj_list);
+            HDfree(obj_list);
             return -1;
         }
 
@@ -168,11 +168,11 @@ int h5repack_addfilter(const char* str,
     else
         options_add_filter(obj_list, n_objs, filter, options->op_tbl);
 
-    free(obj_list);
+    HDfree(obj_list);
     return 0;
 }
 
-
+
 /*-------------------------------------------------------------------------
 * Function: h5repack_addlayout
 *
@@ -234,13 +234,13 @@ int h5repack_addlayout(const char* str,
         &pack,
         options->op_tbl);
 
-    free(obj_list);
+    HDfree(obj_list);
     return 0;
 }
 
-/* Note: The below copy_named_datatype(), named_datatype_free(), copy_attr() 
- * were located in h5repack_copy.c as static prior to bugfix1726. 
- * Made shared functions as copy_attr() was needed in h5repack_refs.c. 
+/* Note: The below copy_named_datatype(), named_datatype_free(), copy_attr()
+ * were located in h5repack_copy.c as static prior to bugfix1726.
+ * Made shared functions as copy_attr() was needed in h5repack_refs.c.
  * However copy_attr() may be obsoleted when H5Acopy is available and put back
  * others to static in h5repack_copy.c.
  */
@@ -271,21 +271,21 @@ hid_t copy_named_datatype(hid_t type_in, hid_t fidout, named_dt_t **named_dt_hea
     if(H5Oget_info(type_in, &oinfo) < 0)
         goto error;
 
-    if(*named_dt_head_p) 
+    if(*named_dt_head_p)
     {
         /* Stack already exists, search for the datatype */
         while(dt && dt->addr_in != oinfo.addr)
             dt = dt->next;
 
         dt_ret = dt;
-    } 
-    else 
+    }
+    else
     {
         /* Create the stack */
         size_t  i;
 
         for(i=0; i<travt->nobjs; i++)
-            if(travt->objs[i].type == H5TRAV_TYPE_NAMED_DATATYPE) 
+            if(travt->objs[i].type == H5TRAV_TYPE_NAMED_DATATYPE)
             {
                 /* Push onto the stack */
                 if(NULL == (dt = (named_dt_t *) HDmalloc(sizeof(named_dt_t))))
@@ -298,7 +298,7 @@ hid_t copy_named_datatype(hid_t type_in, hid_t fidout, named_dt_t **named_dt_hea
                 dt->id_out = -1;
 
                 /* Check if this type is the one requested */
-                if(oinfo.addr == dt->addr_in) 
+                if(oinfo.addr == dt->addr_in)
                 {
                     HDassert(!dt_ret);
                     dt_ret = dt;
@@ -308,7 +308,7 @@ hid_t copy_named_datatype(hid_t type_in, hid_t fidout, named_dt_t **named_dt_hea
 
     /* Handle the case that the requested datatype was not found.  This is
      * possible if the datatype was committed anonymously in the input file. */
-    if(!dt_ret) 
+    if(!dt_ret)
     {
         /* Push the new datatype onto the stack */
         if(NULL == (dt_ret = (named_dt_t *) HDmalloc(sizeof(named_dt_t))))
@@ -323,7 +323,7 @@ hid_t copy_named_datatype(hid_t type_in, hid_t fidout, named_dt_t **named_dt_hea
 
     /* If the requested datatype does not yet exist in the output file, copy it
      * anonymously */
-    if(dt_ret->id_out < 0) 
+    if(dt_ret->id_out < 0)
     {
         if (options->use_native==1)
             dt_ret->id_out = h5tools_get_native_type(type_in);
@@ -365,7 +365,7 @@ int named_datatype_free(named_dt_t **named_dt_head_p, int ignore_err)
 {
     named_dt_t *dt = *named_dt_head_p;
 
-    while(dt) 
+    while(dt)
     {
         /* Pop the datatype off the stack and free it */
         if(H5Tclose(dt->id_out) < 0 && !ignore_err)
@@ -418,6 +418,8 @@ int copy_attr(hid_t loc_in,
     H5O_info_t oinfo;             /* object info */
     int        j;
     unsigned   u;
+    hbool_t    is_ref=0;
+    H5T_class_t type_class = -1;
 
     if(H5Oget_info(loc_in, &oinfo) < 0)
         goto error;
@@ -451,7 +453,7 @@ int copy_attr(hid_t loc_in,
 
             /* Copy named dt */
             if((wtype_id = copy_named_datatype(ftype_id, fidout, named_dt_head_p,
-                    travt, options)) < 0) 
+                    travt, options)) < 0)
             {
                 H5Fclose(fidout);
                 goto error;
@@ -484,15 +486,37 @@ int copy_attr(hid_t loc_in,
             goto error;
 
         /*-------------------------------------------------------------------------
-        * object references are a special case
-        * we cannot just copy the buffers, but instead we recreate the reference
-        * this is done on a second sweep of the file that just copies
-        * the referenced objects
+        * object references are a special case. We cannot just copy the buffers,
+        * but instead we recreate the reference.
+        * This is done on a second sweep of the file that just copies the referenced
+        * objects at copy_refs_attr()
         *-------------------------------------------------------------------------
         */
+        type_class = H5Tget_class(wtype_id);
+        is_ref = (type_class == H5T_REFERENCE);
+        if (type_class == H5T_VLEN ||type_class == H5T_ARRAY ) {
+        	hid_t base_type = -1;
+        	base_type = H5Tget_super(ftype_id);
+        	is_ref = (is_ref || (H5Tget_class(base_type)==H5T_REFERENCE));
+        	H5Tclose(base_type);
+        }
 
-        if(H5T_REFERENCE == H5Tget_class(wtype_id)) {
-            ;
+        if (type_class == H5T_COMPOUND) {
+        	int nmembers = H5Tget_nmembers(wtype_id) ;
+        	for (j=0; j<nmembers; j++) {
+        		hid_t mtid = H5Tget_member_type( wtype_id, j );
+        		H5T_class_t mtclass = H5Tget_class(mtid);
+        		H5Tclose(mtid);
+
+        		if (mtclass==H5T_REFERENCE) {
+        			is_ref = 1;
+        			break;
+        		}
+        	} /* for (j=0; i<nmembers; j++) */
+        } /* if (type_class == H5T_COMPOUND) */
+
+        if(is_ref) {
+            ; /* handled by copy_refs_attr() */
         }
         else {
             /*-------------------------------------------------------------------------
@@ -522,9 +546,9 @@ int copy_attr(hid_t loc_in,
             if(H5Aclose(attr_out) < 0)
                 goto error;
 
-            /* Check if we have VL data in the attribute's  datatype that must
+            /* Check if we have VL data and string in the attribute's  datatype that must
              * be reclaimed */
-            if(TRUE == H5Tdetect_class(wtype_id, H5T_VLEN))
+            if (TRUE == h5tools_detect_vlen(wtype_id))
                 H5Dvlen_reclaim(wtype_id, space_id, H5P_DEFAULT, buf);
             HDfree(buf);
             buf = NULL;
@@ -554,13 +578,13 @@ int copy_attr(hid_t loc_in,
 error:
     H5E_BEGIN_TRY {
         if(buf) {
-            /* Check if we have VL data in the attribute's  datatype that must
+            /* Check if we have VL data and string in the attribute's  datatype that must
              * be reclaimed */
-            if(TRUE == H5Tdetect_class(wtype_id, H5T_VLEN))
+            if (TRUE == h5tools_detect_vlen(wtype_id))
                 H5Dvlen_reclaim(wtype_id, space_id, H5P_DEFAULT, buf);
 
             /* Free buf */
-            free(buf);
+            HDfree(buf);
         } /* end if */
 
         H5Tclose(ftype_id);
@@ -980,7 +1004,7 @@ static const char* get_sfilter(H5Z_filter_t filtn)
         return "SOFF";
     else {
         error_msg("input error in filter type\n");
-        exit(EXIT_FAILURE);
+        HDexit(EXIT_FAILURE);
     }
 }